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Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Mesoporphyrin IX and Substrate 4-bromo-ortho-cresol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2 M Ammonium Sulphate,
MPEG 2000, 29-33%
Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.867 α = 90 b = 68.078 β = 90 c = 67.631 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 30.42 99.42 0.995 12 2.4 20289
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.01 0.649
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3IXF 1.954 30.42 19160 1013 99.418 0.198 0.1952 0.2026 0.2418 0.2422 25.718
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.16 -0.382 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 25.075 r_dihedral_angle_3_deg 17.86 r_dihedral_angle_other_2_deg 16.685 r_dihedral_angle_other_1_deg 15.041 r_dihedral_angle_1_deg 6.107 r_lrange_it 5.002 r_lrange_other 4.991 r_scangle_it 2.113 r_scangle_other 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 25.075 r_dihedral_angle_3_deg 17.86 r_dihedral_angle_other_2_deg 16.685 r_dihedral_angle_other_1_deg 15.041 r_dihedral_angle_1_deg 6.107 r_lrange_it 5.002 r_lrange_other 4.991 r_scangle_it 2.113 r_scangle_other 2.097 r_angle_refined_deg 1.795 r_angle_other_deg 1.435 r_mcangle_it 1.389 r_mcangle_other 1.389 r_scbond_it 1.325 r_scbond_other 1.311 r_mcbond_it 0.876 r_mcbond_other 0.874 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.252 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_other 0.23 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.086 r_xyhbond_nbd_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_symmetry_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing